Description Usage Arguments Details Value Author(s) References Examples
View source: R/ZhaoImmuneLiverData.R
Obtain the human liver immune single-cell RNA-seq data from Zhao et al. (2020).
1 | ZhaoImmuneLiverData(location = TRUE, filter = FALSE)
|
location |
Logical scalar indicating whether genomic coordinates should be returned. |
filter |
Logical scalar indicating if the filtered subset should be returned. |
Column metadata contains various cell labels as provided by the authors. Some of these labels required assembly on our part:
The broad
label was assigned to each barcode based on whether that barcode was present in each *_identities.tsv.gz
in GSE125188's supplementary files.
For each cell barcode that was present in one of these files, the fine
label was generated from the Group
annotations inside that file.
We guessed the sample
for each cell by assuming that the GEM group numbers match the order of samples in GSE125188.
We also assumed that “donor 4” is a typo, given that the paper only mentions 3 donors.
If location=TRUE
, the coordinates of the Ensembl gene models are stored in the rowRanges
of the output.
Note that this is only performed if ensembl=TRUE
.
If filter=TRUE
, only cells that have been used in the original analysis are returned.
Otherwise, the cells used are specified in the retained
column of the colData
.
All data are downloaded from ExperimentHub and cached for local re-use.
Specific resources can be retrieved by searching for scRNAseq/zhao-immune-liver
.
A SingleCellExperiment object with a single matrix of UMI counts.
Aaron Lun
Zhao J et al. (2020). Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell Discov 6, 22.
1 | sce.zhao <- ZhaoImmuneLiverData()
|
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